Plateau Grass and Greenhouse Flower? Distinct Genetic Basis of Closely Related Toad Tadpoles Respectively Adapted to High Altitude and Karst Caves
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Sampling
2.3. RNA Extraction and Sequencing
2.4. Quality Control, Sequence Assembly and Annotation
2.5. Phylogenetic Reconstructions
2.6. Accelerated Evolutionary Rates Analyses
2.7. Identifying Fast Evolving Genes (FEGs) and Positively Selected Genes (PSGs)
2.8. Protein Structure Homology Modelling
3. Results
3.1. Gene Homology Analyses
3.2. Phylogenetic Reconstructions
3.3. Accelerated Evolutionary Rates Analyses
3.4. Fast Evolving Genes (FEGs) and Positively Selected Genes (PSGs)
3.5. Candidate Genes for Adapting to High Elevation and Karst Caves
3.6. Amino Acid Substitutions of XRCC6 Gene in S. boulengeri
4. Discussion
4.1. Genetic Signals for High-Elevation Adaptation of Toad Tadpoles on Tibetan Plateau
4.2. Signals of High-Elevation Adaptation Increasing with Elevation in the Toad Species
4.3. Explanations on Genetic Adaptation of the Cave Species O. Rhodostigmatus
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Species | FEGs | PSGs |
---|---|---|
S. boulengeri | GFM1, MTIF2, ERAL1, GFM2, MRPL37, MRPS35, MRPS7, MRPS28, OXA1, C7orf55, NDUFA9, NDUFA12, SLC25A32, SLC25A10, RECQL, XRCC6, UBE2M, NSMCE1, RFC1, DDX1, CLDN3, SLC35C2, CHCHD2, ABCB6, CLPB, NPTX1, CHRND, SIGIRR, FAM58A, PMF1, AVEN, E2F6, C10orf11, VPS39 | PDE12, ERAL1, NDUFA9, RECQL, AMN1, AVEN, CAPG, ARMC5, FAM58A, LRMDA, PSMB8, UBE2M, MRPS35 |
O. major | MTPAP, MTIF2, SCO1, ERAL1, POLH, RFC1, MRGBP, RAB8B, DUSP22 | SCO1, ERAL1, RFC1, MRGBP, HSF2, DUSP22, IDS |
O. popei | XRCC6, PYROXD1, TFR2, LACTB2, TECTA | ACP7, TAMM41, XRCC6, PYROXD1, TFR2, LACTB2, PINX1 |
O. omeimontis | PYROXD2, TSG101, EIF1AD, GCH1 | MTG1, CRLS1, GCH1 |
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Chang, L.; Zhu, W.; Shi, S.; Zhang, M.; Jiang, J.; Li, C.; Xie, F.; Wang, B. Plateau Grass and Greenhouse Flower? Distinct Genetic Basis of Closely Related Toad Tadpoles Respectively Adapted to High Altitude and Karst Caves. Genes 2020, 11, 123. https://doi.org/10.3390/genes11020123
Chang L, Zhu W, Shi S, Zhang M, Jiang J, Li C, Xie F, Wang B. Plateau Grass and Greenhouse Flower? Distinct Genetic Basis of Closely Related Toad Tadpoles Respectively Adapted to High Altitude and Karst Caves. Genes. 2020; 11(2):123. https://doi.org/10.3390/genes11020123
Chicago/Turabian StyleChang, Liming, Wei Zhu, Shengchao Shi, Meihua Zhang, Jianping Jiang, Cheng Li, Feng Xie, and Bin Wang. 2020. "Plateau Grass and Greenhouse Flower? Distinct Genetic Basis of Closely Related Toad Tadpoles Respectively Adapted to High Altitude and Karst Caves" Genes 11, no. 2: 123. https://doi.org/10.3390/genes11020123
APA StyleChang, L., Zhu, W., Shi, S., Zhang, M., Jiang, J., Li, C., Xie, F., & Wang, B. (2020). Plateau Grass and Greenhouse Flower? Distinct Genetic Basis of Closely Related Toad Tadpoles Respectively Adapted to High Altitude and Karst Caves. Genes, 11(2), 123. https://doi.org/10.3390/genes11020123